Whole-Genome Phenotype Prediction with Machine Learning: Open Problems in Bacterial Genomics
This problem affects researchers and scientists working in bacterial genomics, particularly those seeking to identify causal genetic mechanisms underlying bacterial traits.
The authors tackled the problem of predicting bacterial phenotypes from genotypes using machine learning, achieving high accuracy scores but struggling with extracting meaningful causal mechanisms, with no concrete numbers reported. The result highlights the challenge of relying on pattern recognition in high-dimensional bacterial genomics data.
How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to extract any meaning from the predictive models are found to be corrupted by falsely identified "causal" features. Relying solely on pattern recognition and correlations is unreliable, significantly so in bacterial genomics settings where high-dimensionality and spurious associations are the norm. Though it is not yet clear whether we can overcome this hurdle, significant efforts are being made towards discovering potential high-risk bacterial genetic variants. In view of this, we set up open problems surrounding phenotype prediction from bacterial whole-genome datasets and extending those to learning causal effects, and discuss challenges that impact the reliability of a machine's decision-making when faced with datasets of this nature.